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Tagged Files for CombineVariants in Queue?
The 3.2 CombineVariants Queue extension does not seem to pass through the TaggedFile information. I assume the extension generator is not recognizing the particular input type used by CombineVariants…
this.V = List(new TaggedFile("file1.vcf","file1"), new TaggedFile("file2.vcf","file2"))
in a Scala class that extends CombineVariants will produce:
-V file1.vcf -V file2.vcf
without the tags.